Questions tagged [reference-request]

This tag is for questions looking for a single specific, or a small number of (citable) references.

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26
votes
3answers
291 views

Where is the extended Hückel method (EHM) still used today?

The extended Hückel method (EHM) proved to be very useful through time, but there are better and affordable models today. One interesting thing about the model is the independence of the Hamiltonian ...
26
votes
2answers
407 views

How is Julia used in Materials Modeling?

What are the main uses and applications of Julia in Materials Modeling? Python for example is used in codes such as kwant, ...
25
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2answers
316 views

What is the current status of machine learning applied to materials or molecular systems?

I heard that machine learning techniques on materials use a large quantity of data to make predictions of a variety of features; for instance, a crystal structure. Data collected from empirical or ...
23
votes
1answer
132 views

Benchmark Timings of Machine Learning Potentials vs Molecular Mechanics Force Fields

Machine learning is an increasingly common tool for developing force fields for molecular dynamics simulations. It's not totally clear what should be considered a machine-learning potential, but let's ...
22
votes
5answers
366 views

What functions other than Gaussians are used for orbital basis sets?

The Gaussian function $\propto\exp((x-a)^2/b)$ with $b>0$ is one of the most common functions used in molecular modelling (e.g. Gaussian type orbitals). What are some examples of applications of ...
22
votes
4answers
297 views

Available methods and codes for materials discovery / crystal structure prediction?

There are many open databases and projects that allow you to access computed crystal structures of experimentally known compounds, registered in the Inorganic Crystal Structure Database (ICSD). These ...
22
votes
3answers
181 views

Examples for results obtained from modeling materials having had a direct impact in discovery of new materials

Materials Modeling helps give theoretical insight into the working of various materials and in turn helps enhance the working of these materials. But are there examples of discovery of new materials ...
22
votes
2answers
476 views

Create a new DFT functional from experimental data

This is my first time here and I think you can help me. I would like to try (just for fun) to create a new DFT functional starting from experimental data. Do you have any manual, procedure or ...
22
votes
2answers
243 views

What are the different ways of calculating dispersion constants?

There are many different dispersion corrections out there. The most famous is D3 [1] (and the new D4 [2]), but there's probably other approaches too. The dispersion energy can be written as: $$ E_{\...
22
votes
1answer
170 views

What are some examples of active learning methods used in atomistic machine learning?

Many machine learning attempts in atomistic applications (see this answer) seem to parameterize models on calculated data (i.e., CCSD(T), DFT, etc.). This approach suggests some automatic procedure ...
22
votes
1answer
123 views

Which basis set families were optimized to give the lowest possible variational energy for a given number of orbitals?

Dunning's basis set families (such as cc-pVXZ and aug-cc-pCVXZ) were not optimized to give the lowest variational energy for a given number of orbitals. For example the S-type orbitals are optimized, ...
20
votes
6answers
1k views

What are good resources to learn to code for matter modeling?

A little bit of coding can a long way in matter modeling. Coding is not used only to write big programs but can be used for scripting, data processing, automation, and more. But sometimes many ...
20
votes
3answers
1k views

Introduction to protein folding for mathematicians

My background is mostly in (applied) math with healthy doses of physics and computer science. Are there any good introductions to protein folding and its challenges for someone with that kind of ...
20
votes
2answers
242 views

What are the great unsolved questions in Matter Modeling?

This is inspired from an amazingly successful question on Operations Research Stack Exchange: What are the great unsolved problems in operations research? Wikipedia has some huge lists of: Unsolved ...
20
votes
2answers
193 views

Is there a list of all universality classes for phase transitions with examples of each?

I've often had this problem: I have a model that has a phase transition in it, but I don't know what universality class it falls into or what the universality class is called. Is there anywhere on ...
19
votes
1answer
107 views

Are there any High-Throughput studies that aim to discover High Tc superconductors?

High-Throughput materials modeling based on Density Functional Theory has become very popular recently. If, for example, we search "High-Throughput Perovskites" in Google Scholar, we get over ~14,000 ...
19
votes
1answer
93 views

Database or repository with values for the Hubbard potential U?

The Materials Project and other materials databases have a nice periodic table on their home page that allows you to search for compounds. For some materials, they give an empirical $U$ value used to ...
18
votes
4answers
592 views

References for Molecular Dynamics?

I am new to the world of Molecular Dynamics (zero practical experience), and I know that a starting point to really go into the back-bone of MD is Statistical Mechanics (took a semester course in ...
18
votes
5answers
413 views

What are the types of SCF?

Many of us know the most common types of SCF (though we can do better than Wikipedia at explaining them): RHF (Restricted Hartree-Fock), RKS (Restricted Kohn-Sham) [link to answer] UHF (Unrestricted ...
18
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3answers
422 views

Are there any online course/video lectures available on Density functional theory?

Please mention good online video lectures on theoretical foundations and practical implementation of DFT.
18
votes
1answer
141 views

What is the state of the art in terms of local atomic environment descriptors for machine learning?

A lot of atomistic machine learning deals with correctly describing atomic neighborhood environments by vectors or fingerprints (see, e.g. J. Chem. Phys. 149, 244102 (2018), Phys. Rev. B 87, 184115 (...
18
votes
1answer
214 views

Promising functionals for transition metal chemistry

I'm looking to get your opinions on the most promising density functionals to use for thermochemistry and kinetics of transition metal complexes. However, as eloquently laid out by Tom Manz on this ...
17
votes
1answer
114 views

Benchmark transition state geometries in condensed phases

I'm seeking references/benchmarks for transition state geometries of reactions in condensed phases like crystals, zeolites, or surfaces. Basically the system just needs to be considered big, yet ...
17
votes
1answer
205 views

What is the difference between BDFT and CDFT (magnetic-field DFT and current DFT)?

Following the previous discussion on DFT in strong fields, I would like to ask about the difference between those two alternatives (BDFT and CDFT). By CDFT I do not mean (constrained DFT, but current ...
16
votes
6answers
308 views

What are the applications of chemical graph theory?

Graph theory was originally introduced in computer science to study data structure. Chemists also introduced graph theory to study the relation between structure and properties for molecular compounds....
16
votes
3answers
1k views

I am a beginner in DFT. What are some resources that could help me to learn the basics?

I am a beginner in DFT. Please suggest me some good material to understand the basics.
16
votes
2answers
163 views

State of the art in computational materials design

With the advent of more computational power than ever in the recent years, interest in in silico design of interesting compounds has grown as well. I am wondering about the state of the art for the ...
16
votes
3answers
177 views

What are the types of MCSCF?

Similar to: What are the types of SCF? What are the types of Quantum Monte Carlo? What are the types of ab initio Molecular Dynamics? What are the types of pseudopotentials? What are the types of DFT?...
16
votes
1answer
108 views

What are typical RPA capabilities of plane-wave codes?

Plenty of standard plane-wave codes are able to compute correlation energies on top of DFT solutions using the random-phase approximation (RPA). I was wondering what the typical capabilities are in ...
15
votes
2answers
185 views

Is there any good review paper on the density matrix renormalization group (DMRG) method?

I would appreciate if someone could recommend me good review literature on the density matrix renormalization group (DMRG) method, especially for magnetic systems.
15
votes
3answers
218 views

What ab initio methods are better suited to modelling disorder in materials?

In contrast to the perfect periodic bulk materials, now computational approaches are moving towards modeling ‘real’ materials or solid solutions with dopants, dislocations, grain boundaries, and ...
15
votes
1answer
124 views

What is the definition of ergodicity in Monte Carlo?

I've been writing a manuscript about the breakdown of ergodicity in single spin flip Metropolis algorithm Monte Carlo arXiv:2001.09268. The definition I have been using is: a Markov process is ...
15
votes
1answer
60 views

What are good resources to study crystallographic defects in different dimensional systems and their topological dimensionality?

I wonder if there are any books or resources that may address one or more of the following questions: What kinds of defects are important for topology? Especially crystallographic defects. How do ...
15
votes
1answer
98 views

Types of Discrete molecular models

It is often assumed in cheminformatics that molecules with similar physical structure tend to have similar chemical properties [1]. Based on this, our group has used discrete graphs as a model for the ...
14
votes
2answers
116 views

What is the largest system for which vibrationally resolved electronic spectra have been simulated using ML-MCTDH?

Multi-layer Multi-configuration time-dependent Hartree (ML-MCTDH) is a method widely used for simulation of vibrationally resolved electronic spectra that incorporate the coupling between vibrational ...
14
votes
1answer
222 views

Software recommendations for passivating structures

I am looking for an open-source library that allows to passivate a structure, ideally starting from a xyz-file. QuantumATK provides a function like this. However, this is not an option at the moment. ...
13
votes
2answers
230 views

Hubbard U correction for Copper

I am reviewing some information in the Materials Project and notice that they do not use DFT+U to model copper oxides. Since the methodology for fitting U is largely based on the 2006 Ceder paper, I ...
13
votes
1answer
77 views

What are the modelling techniques that can be used for simulating microstructure evolution in materials?

I am aware that the Potts Model can be used to simulate grain growth, and that Phase Field Models have also been very successful. What are the advantages and limitations of these models? What are the ...
13
votes
1answer
129 views

TS-search with explicit solvent

I'm looking for an advice how the best to set up the system and optimize a transition state with explicit solvent. I believe that solvent molecules are participating in the reaction by specific ...
13
votes
1answer
115 views

What progress has been made in modelling photocatalytic reactions on semiconductor surfaces?

For example, are there any methods to allow for modeling of photo-oxidation or photo-reduction of a compound on a semiconductor surface? It appears there has been a lot of work on the bulk properties ...
12
votes
3answers
520 views

Is the DYNAMO code developed by LAMMPS still available?

In 2013 it was stated that v8.8 of DYNAMO was the version mostly used for the last 10-12 years. However I am struggling to find the code repository. It was developed by the LAMMPS developers and is ...
12
votes
2answers
466 views

What is Surface termination and how to make surface termination of a crystal structure?

I want to calculate the surface energy of CuO and for that, I've asked CuO (monoclinic) crystallographic plane and their relaxed surface energy. But for the lack of knowledge of the surface ...
12
votes
1answer
367 views

Are there any good books to learn how to use DFT+U?

I am interested in learning how to do DFT+U calculations and was wondering if anyone has any good recommendations for books or articles.
12
votes
2answers
94 views

What are real examples where fractals were used in Matter Modeling?

A fractal is, accordingly Oxford English Dictionary: A curve or geometric figure, each part of which has the same statistical character as the whole. Fractals are useful in modeling structures (such ...
12
votes
1answer
218 views

How does the atomic arrangement look like in a compound that has partial/mixed site occupancies

I am working on modelling of a material that has partial/mixed site occupancies. For example consider the tetragonal (P4mm) compound $\ce{(Ba_{0.67}Sr_{0.33})TiO3}$. Following is the atomic ...
12
votes
1answer
83 views

Derivation of logarithmic singularity that causes the Kohn anomaly

The basis of the Kohn anomaly is that a logarithmic singularity at $q=2k_\rm F$ (where $k_\rm F$ is the radius of the Fermi sphere) causes extreme fluctuations of the dielectric function about that ...
12
votes
1answer
91 views

Theoretical origins of stereochemistry

What are the current theories of computational chemistry for studying homochirality (for example the phenomenon discussed here, here and in many other places)? Electroweak chemistry has been developed ...
12
votes
1answer
88 views

Recent developments in QM/MM for Molecular Dynamics

I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
12
votes
0answers
50 views

What are good references to learn how to model heterostructures using DFT? [closed]

I am interested in modeling heterostructures using DFT. What are some good references to start learning?
11
votes
1answer
207 views

What are good resources to learn Materials Modeling? [closed]

I wonder if there are any books or resources to start learning Materials modelling using methods density functional theory quantum monte carlo molecular dynamics